7  Appendix: Creation of a supplementary table

✓ All shared objects created successfully from _objects.R

During data analysis for a publication (and other scientific outputs), we may want to share some of the intermediary outputs we have generated - for example, some summarized data may provided as a supplementary material with our publication. We do not need to start from scratch - we simply proceed further with our project. There are probably multiple ways to achieve the goal of this section, we will use {openxlsx} package.

library(openxlsx2)

1. We, fill create a new workbook and add a new sheet with defined name to it.

wbook <- wb_workbook()

wbook$add_worksheet("Table S1")

2. We will populate it with data. Before doing so, we will modify the input data frame a bit - for example, change column names and remove the HTML syntax fro the type column. We can also define number of decimal places.

export_veg_summarized <- veg_summarized |>
  mutate(type = gsub("<sub>|</sub>", "", type))

export_veg_summarized <- export_veg_summarized |>
  rename(
    "mean delta" = mean_d,
    "SD delta" = sd_d,
    "N measurements" = n_plants
  )

wbook <- wbook$add_numfmt(
  sheet = 1,
  dims = wb_dims(
    # Target all rows from Row 2 (data) to the end
    rows = 2:(nrow(export_veg_summarized) + 1),
    cols = 5:6
  ),
  # Use the standard Excel number format for two decimal places
  numfmt = "0.000"
)

wbook$add_data("Table S1", export_veg_summarized)

3. We will introduce a minimal formatting to the data in workbook: column headers in bold and family names in italics.

wbook <- wbook$add_font(dims = wb_dims(rows = 1, cols = 1:ncol(export_veg_summarized)), bold = T)

wbook$add_font(dims = wb_dims(rows = 2:(nrow(export_veg_summarized) + 1), cols = 1), italic = T)

4. Finally, we can export the workbook into an XLSX file.

dir.create("outputs")

wb_save(wbook, file = "outputs/Supplementary_data.xlsx")